Chaos Theory
by ArcHammer123
Summary: Eight years after that famous summer, much has changed and much hasn't. But things are about change in ways no one can imagine. Taking "Mission Marvel" to its logical conclusion, this story isn't really a cross over since Mission Marvel places the Phineas and Ferb Universe within the Marvel Universe.
1. Chapter 1

The sunlight crept in through the open curtains, filling the bedroom with a morning glow. If anyone had been in the room, they would have found it rather beautiful. The bedroom's occupant had left over an hour ago, for this was an important day.

Isabella Garcia-Shapiro had left her house well before sunrise, she had an appointment on the other end of town. It was her birthday, and for the past few years it had been a tradition for her to meet her friends for morning coffee. It was usually just her old Fireside Girls Troop, since her other friends were often busy getting some huge surprise ready.

Isabella was anticipating a massive event, since that was Phineas' usual style. Of course, what she really wanted was just some alone time with him. In the final months of the school year, having been encouraged (and pestered) by her friends, Isabella had finally told Phineas her feelings for him. As chance would have it, Phineas was going to ask her out that very same day. Of course it wasn't chance, it was their friends collaborating. They always said that if they lived in a tv show, that the entire fanbase would ship Phineas and Isabella.

Isabella was the last to arrive, but this was normal on these special outings. Gretchen and Adyson usually showed up first to make sure their usual booth was available. Isabella took a seat next to Gretchen, still amazed at how the girl who had been the shortest of them all was now easily the tallest.

"Happy Birthday Isabella." she said, giving her friend a hug.

"Thanks, to all of you. I know how much work goes into these meets."

"It's nothing, really." Holly spoke up.

"Anything for our great leader." Chell added.

"I haven't been your leader for years." Isabella chided. But she knew that these girls would follow her to the ends of the earth and beyond if she asked.

The arrival of drinks interrupted any potential response. Most of the girls had lattes of some sort, though Ginger had tea and Milly just had water, since she never really liked hot drinks. Isabella took her coffee straight black, if her spoon didn't stand straight up, she knew it wasn't worth drinking. Katie was the first to break the silence.

"So, have any idea what Phineas and Ferb are up to?"

"Yeah." Adyson said. "This isn't just any birthday, this your sixteenth birthday."

"And your first birthday since you and Phineas became an item." Gretchen added.

"I don't know anymore than you do, unless you're all in on it too." Isabella knew that the girls were often privy to secrets that Isabella didn't know, although it was often a risk to tell Milly any secret. She couldn't keep a secret to save her life.

The girls faked offense at the accusation, and they all had a good laugh.

* * *

On the other side of town, across the street from the bedroom Isabella wasn't in, another group were talking about Isabella's birthday celebrations. Phineas and his stepbrother Ferb had gathered their team (minus Isabella and the Fireside Girls) to their backyard.

"Alright everyone, listen up." Phineas said. "The girls will keep Isabella at the coffee shop for three more hours at most. That gives us two hours to get everything ready. Buford and Baljeet, you get the the outflow ditches ready. We don't want the yard flooding during phase 3. Django and Balthazaar, you're on decoration detail. A few things have places set up but for the most part just decorate however you'd like. Irving, start getting the backup generators in place. I don't want a repeat of last year. Ferb and I will handle the stage. Any questions?"

"Yeah," Buford spoke up. "Where's Perry?"

* * *

Perry ducked out sight behind the tree, quickly donning his fedora as he made his way through a secret door in the tree. He smiled to himself during the lift ride down to his lair. He knew how much Phineas cared for Isabella, and Perry knew the what the real surprise for Isabella was. After the big celebrations were over, Phineas was going to take Isabella for a totally normal walk around the neighborhood. That would be the perfect gift.

As the lift neared the bottom, Perry put on his usual austere persona. He took his job seriously, not quite as much as that old stick in the mud Peter the Panda. Still, sometimes Major Monogram and Carl's antics got a little tiresome. Carl had long since been promoted to paid facility manager for Monogram, though he still did much of the same work he always had. Although Monty and Vanessa were usually there to help him out.

Perry sat down in his chair as the image of Major Monogram appeared on the screen.

"Good morning Agent P. We've been monitoring activity on the Evil Scientist Network, and we've discovered something rather disturbing. It seems that someone is trying to refound L.O.V.E. M.U.F.F.I.N."

Perry grimaced. The League Of Villainous Evildoers Manically United For Frightening Investments In Naughtiness had been defunct for years, ever since almost the entire organization had been arrested for crimes against humanity. It wasn't a good day for OWCA either, as the agency had almost been destroyed along with L.O.V.E. M.U.F.F.I.N.

Monogram continued. "We've been trying to identify who could be behind this. A few members of L.O.V.E. M.U.F.F.I.N. escaped the arrests and went to ground, but they haven't been up to much in years. Just so we can cover all our bases, I'm sending you to Dr. Doofenshmirtz. I don't think he's behind this, but he might know who is. Good luck Agent P."

Perry gave his boss a salute before jumping into his hovercar.

* * *

Meanwhile and far away, a hooded figure sat alone. He glanced out the only window in sight, watching the rain pour down outside. The roof was leaky, so he could feel the occasional drop of rain on his shoulders.

Suddenly he felt a vibration in his pocket. Pulling out the burner cellphone, he answered.

"Yeah, I'm here."

"Good. The tracker just registered that the package has arrived in Danville, it should get to its destination by the evening post."

The hooded man breathed a sigh of relief.

"Are you sure this will work?" the voice on the other end asked. "What if she doesn't remember?"

"Oh she'll remember. She may not want to, but she will. I just hope she can crack it enough to raise the flag."

"We'll have to see. Is it raining where you are too?"

"Maybe. I think I've been here long enough. I'm going to the next place. I'll contact you with the new number once I'm there."

"Roger that. Good luck."

"Thanks."

The hooded man hung up and started gathering his things. He traveled light, and was soon on his way. Ordinarily he wouldn't have left any trace of his presence. But this time, he was hoping someone would discover that he had been there.

 _Let's just hope it's the right people_ he thought, as he tossed the phone into a nearby ditch.

Authors Note: Chell is the eighth member of Troop 46231. She is usually known as Unknown Fireside Girl Blonde.


	2. Chapter 2

"Isabella, are you sure you don't want to go visit the clubhouse?" Gretchen was getting a little nervous. They had stalled Isabella for a while, but the boys might not be ready yet.

"We've already went to visit the lodge, we don't need to hike all the way out into the woods."

Isabella knew they were stalling, but it been hours already and Phineas was probably done by now.

"Fair enough, let's head to your place."

The girls walked back towards Maple Street, chatting about this and that as they went. Ginger had slowed a bit, and she seemed to have a headache of some sort.

"I tell you, that's why I don't drink caffeinated drinks." Milly chided.

"It's also why you can't stay awake at times, no energy."

They all had a good laugh as they arrived as Isabella's house. Holly had slipped away unnoticed to go check that everything was ready. After giving the all clear to Gretchen, the group approached the door.

* * *

Perry landed his hovercar on Doofenshmirtz's terrace and made his way inside. It was quiet, which was immediately concerning. Though Doofenshmirtz had long given up evil, he was still a tinkerer and his home usually had all sorts of noises as he and Norm worked on something or other.

But now there was no sign of the scientist or the robot. Glancing around, Perry spotted a table set up in the corner with a tape recorder. Perry hit play and Doof's voice started talking.

"Hello Perry the Platypus. If you're hearing this, it's because I'm not home right now. I have gone the store to pick up some rice pudding. I really should hire a emp to do those sorts of things. Hey, remember that time you came to thwart me when you wore a emp disguise? Oh, those were the days. I think I still have the disguise you wore in my startle space. We should really go look for it. Anyway, I have to go, see you later Perry."

Perry stood for a moment, working over what Doofenshmirtz had said. Something wasn't right; Doofenshmirtz hated rice pudding. And why did he keep leaving the t out of temp? Wishing to shed some light on the matter, Perry headed for the heavy light switch lever on the floor. For some reason the lights didn't come on. Perry was about to assume Doof had just blown the wiring on some new project, when suddenly it made sense. Doofenshmirtz hadn't been saying temp, he had been saying EMP, as in an Electromagnetic Pulse weapon. That explained why the lights weren't working, and why the message was on an analog tape recorder. But why would an EMP go off in Doofenshmirtz's lab.

 _I think I still have the disguise you wore in my startle space. We should really go look for it._

Hoping that the key to this whole thing might be there, Perry headed for the startle door.

* * *

Isabella hadn't taken a full step through the door before the lights blazed on.

"HAPPY BIRTHDAY, ISABELLA!"

"Oh, thanks you guys." Isabella said, although she had kind of expected it.

Phineas stepped forward and led Isabella to the backyard.

"Oh Phineas, you really went all out for this didn't you?"

"Nothing less would do. Let's get our seats, Love Händel will do a few numbers before lunch. Then we have a full buffet set up with all your favorites, then some more music."

 _This is going to be a birthday to remember._ Isabella thought to herself.

* * *

Perry stepped up to the door, hesitating at the knob. Obviously something bad had happened to Doofenshmirtz, possible having to do with L.O.V.E. M.U.F.F.I.N.'s mysterious reunification. Steeling himself for the worse, Perry opened the door.

The room seemed no different than it was on the one or two other times Perry had been inside. Almond Brittle and Kleptocracy games were stacked as high as the ceiling, a few lawn chairs were set up, everything looked perfectly normal.

Just as Perry was about to shut the door, a sound came from inside. It was a grinding sound, like metal scraping against tile. It didn't take long to find the source: Norm lay slumped against the wall. The robot couldn't seem to move much other than his right leg, but his eye lights were still on.

"Perry the Platypus, I'm so glad you're here." He said in his usual chipper voice.

"Since you can't talk, I'll just explain what happened. Father and I were working on his latest project when all the sudden the lights went off and I couldn't move. My squirrel generator kept my primary systems online, but my circuitry was completely blown. I couldn't really see what happened next, but there was a lot of shouting and sounds of a struggle. Then I got thrown in here. I heard Father saying something, then it got very quiet. I hope he's ok."

Perry felt sorry for Norm. Doofenshmirtz was Perry's friend, but Norm always say him as a father. After Vanessa moved out, Doofenshmirtz started treating Norm better, and even got used to be called father.

Perry patted Norm on the knee, trying to reassure the robot. He then turned and went back to the main lab. There had to be clues here somewhere, and Perry was going to find them.

* * *

Isabella couldn't help but grin. This had easily been the best birthday ever, and in a rare moment of calm she watched as the sky grew dim as evening drew near. The buffet was mostly exhausted, so Isabella wasn't sure just what Phineas had planned for the rest of the night.

"So, enjoying the party?"

Isabella almost jumped, Phineas was still good at moving silently.

"Immensely. I'm not sure how you're going to be able to top that grand finale. You even kept the power on."

"We took precautions this year. And as for what's next, that's just what I wanted to tell you. You and I are going to take a totally normal, invention-free, romantic walk around town."

Isabella could not contain her joy. They made their way down the street, nodding hello to Mrs. Ferguson the mail carrier, who was delivering the evening post.

* * *

Meanwhile and far away, a man sat in a dark room before a computer screen. He never really cared for light, and there wasn't much anyway since it was still pouring outside. He was working on about ten different projects on the computer screen when his phone rang.

"Hello?" he answered.

"Bravo Hotel." the voice on the other end spoke.

"Mike Tango." the man said, snapping to attention.

"205-4832."

"Copy."

The man hung up, and dialed the number he was given.

"Bravo Hotel." the voice repeated.

"Mike Tango."

"Good. I'll use this phone for about week unless something happens. How's everything on your end?"

"Still good, no word- hold on." a new notification popped up on the screen.

"What is it?" the caller asked.

"The Package. It's arrived."

"Praise be." relief was plain in the hooded man's voice.

"Now it's up to her."

"She'll come through, don't worry. I'm going to go scope out my new place. Call me if anything develops."

"Will do. Have a safe night."

"You know those don't exist anymore." the hooded man laughed mirthlessly.

"Wishful thinking. Good night."

"Good night."

The line went silent. The man sat still for a long while, until he slowly started feeling something he had not felt in a very long time. Hope.


	3. Chapter 3

Gretchen was happy. Everything had gone off without a hitch, and now Isabella was getting her alone time with Phineas.

The doorbell rang, interrupting her thoughts. Opening the door, Gretchen found a large manila envelope.

"What's that?" Katie asked.

"Not sure. It's addressed to Isabella so it's probably a present."

"Probably. Any idea when she and Phineas are getting back?"

"Not for a little while yet. I'm sure it can wait anyway."

* * *

Isabella was very happy. This had easily been the best birthday she'd ever had. She and Phineas had a light dinner on their walk, and now they were all relaxing in her backyard watching the sunset.

"Oh, Isabella, I almost forgot. A package came for you this evening."

"Oh, thanks." Isabella said as she took the manila envelope from Gretchen.

"I don't recognize the return address, but I don't think it's from Danville."

The envelope contained a USB flash drive, and a piece of paper. Isabella read the note aloud:

"Hello Wraith. It's been a long time. I know we haven't had much to do with each other for years, but I need your help. The details are on the flash drive. Gain access to them and you'll find out the rest. Please Wraith, I need you to do this. Lives are on the line.

Sincerely, Black Hole"

The note slipped from Isabella's limp fingers and fluttered to the ground. Isabella stared straight ahead, not moving. Gretchen was out of her chair and at Isabella's side in the blink of eye, snatching up the note and reading it herself. Everyone else passed quick confused glances amongst each other, not sure just what was going on. Phineas was the first to find his voice.

"Isabella? Who is Black Hole?"

At first, Isabella didn't even react. Eventually she seemed to regain some composure.

"I don't know. I'm not sure who this is from or what it's about."

Again, everyone glanced to each other, no one really believing what had been said.

"Perhaps we should see what the USB drive has on it?" Baljeet offered.

"Good idea." Gretchen replied, placing a hand on Isabella's shoulder. "You guys go get it set up, we'll join you in a moment.

Once everyone else had gone inside, Gretchen finally asked the question she'd been asking herself.

"Do you think it's really him?"

"I don't know. If it isn't we have a serious problem. If it is…"

"Then we have several."

* * *

"This doesn't make any sense."

Baljeet had been trying to access the files on the drive, but it wasn't working.

"It's because they're encrypted." Irving answered.

"Why would they be encrypted?" Phineas asked to no one in particular.

Isabella and Gretchen came in at that point. Isabella still looked shaken, and Gretchen had a rather creepy thousand yard stare going. Eventually the latter managed to make eye contact with Phineas.

"So what was on the drive?"

"We don't know. The files are encrypted."

"Can we decrypt them?"

"I can't." Irving said. "This is… extremely secure. But, Albert is really into this sort of stuff. Maybe he could help us."

"It's worth a shot. Do you think he'd take a look at it tonight?" Phineas asked.

"Probably. Let's head over to his apartment."

They decided it would be easiest to walk, since Albert didn't live too far away. Ginger and Baljeet walked together, although Ginger still had her headache. Isabella and Gretchen were in the rear of the group.

"Encrypted files, strange letters… it sounds like him." Gretchen said.

"I know. I just, I'm not sure if I want to admit it." Isabella replied.

"I have to ask, though. If Black Hole is still out there, does that mean Wraith is as well?"

Something very dark came into Isabella's eyes, and Gretchen couldn't help but shudder.

"Wraith is dead. Wraith died eleven years ago."

"You know that's not true, you know-"

Isabella stopped and turned to look Gretchen in the eye. Gretchen was not accustomed to fear. Even during the darkest moments of her life, she had never allowed fear control her. And that made the look that Isabella, Gretchen's oldest and closest friend, gave her all the more terrifying.

"Wraith is dead. Do you understand?"

"Yes, sir."

"Good."

Isabella continued on her way, leaving a very concerned Gretchen to catch up.

* * *

Meanwhile and near at hand, Perry slumped into the Flynn-Fletcher home. He didn't worry about being seen, Linda and Lawrence were out of town for the week, and Candace would be in bed. Which was good, because Perry felt like slumping down in a chair for a few hours. He had gotten no where with either Doofenshmirtz's disappearance or the mysterious reformation of L.O.V.E. M.U.F.F.I.N. than he had this afternoon and frankly, he was in very low spirits.

He was surprised to find Phineas and Ferb's room empty, but he realized that they would probably still be at Isabella's. Deciding to go see what they were up to, and to pay a visit to his friend Pinky, Perry quietly slipped into the Garcia-Shapiro home. He quickly found the entire group huddled around a computer, apparently trying to gain access to some encrypted files. Intrigued, Perry waited and watched as the group left to go consult Irving's brother Albert. Once they were gone Perry walked up and took a look at the screen. Baljeet had copied the two files from the drive to the computer, so Perry took a quick look.

"Don't bother. They're secured pretty tightly."

Perry turned to see Pinky the Chihuahua standing behind him. Although he and Pinky were two very different species, all OWCA agents were taught a shared communication system that OWCA members could communicate with.

"I was taking a look at the screen while they were working, whoever encrypted those files wanted to make sure they were safe." Pinky said.

Perry thought to himself for a moment.

"I think I'll take copies of those files back to Carl, he might know how to crack them."

"Alright, good luck."

* * *

Meanwhile and far away, the hooded man's phone buzzed in his pocket.

"Hello?"

"Good news and potentially bad news. The good news: the camera we put on the flash drive shows that Isabella did get the package. The potentially bad news: all of her friends know about too."

"That was to be expected really. It should be fine, might even be for the best if my suspicions are correct. How did she take it?"

"Isabella? Not well. I don't think she wants to remember Wraith or Black Hole."

"She's probably upset I addressed it to Wraith, but it was the only way she'd know it was really from me."

"I heard her say that Wraith is dead. Are you sure she'll help?"

"Wraith never died. Rejected, yes. Ignored for over a decade, of course. All memory of her shunned and hidden, without a doubt. But Wraith is still alive. Isabella must realize that eventually."

"I hope you're right."

"If I'm not, we won't have to worry about it for very long."


End file.
